I think the key would be that unlike Reddit, where it would be anyone can create a multi-community, it would be up to the mods to tag it then all the back end would do is collect all the communities tagged with that into one multi. When it comes to more niche things, like you pointed out, I think that those things would eventually start evolving organically over time.
But an upside on your down side, say your favorite band is Scottish rock band Texas. They have a sub that is tagged Scottish Bands, you go "huh, let me subscribe to that," and now you found 5 more Scottish rock bands that are similar to Texas that you really dig and have great communities but are all on separate instances across the fediverse.